--- a
+++ b/druggpt_min_multi.py
@@ -0,0 +1,145 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Sun Jul 23 08:12:43 2023
+
+@author: Sen
+"""
+#%%
+import os 
+import argparse
+import shutil
+import logging
+from openbabel import openbabel
+parser = argparse.ArgumentParser()
+parser.add_argument('-d', type=str, default=None, help='Input the dirpath')
+args = parser.parse_args()
+
+dirpath = args.d
+if dirpath[-1] != '/' :
+    dirpath = dirpath + '/'
+#%%
+def create_directory(dir_name):
+    # 使用os.path.exists()检查目录是否存在
+    if not os.path.exists(dir_name):
+        # 如果目录不存在，使用os.makedirs()创建它
+        os.makedirs(dir_name)
+
+input_dirpath = dirpath  #文件夹以/结尾
+dir_name = os.path.basename(os.path.dirname(input_dirpath))
+dir_path = os.path.dirname(os.path.dirname(input_dirpath))
+output_dirpath = os.path.join(dir_path,dir_name+'_min')
+create_directory(output_dirpath)
+logging.basicConfig(level=logging.CRITICAL)
+openbabel.obErrorLog.StopLogging()
+#%%
+def sdf_min(input_sdf, output_sdf):
+    # 创建一个分子对象
+    mol = openbabel.OBMol()
+
+    # 创建转换器，用于文件读写
+    conv = openbabel.OBConversion()
+    conv.SetInAndOutFormats("sdf", "sdf")
+
+    # 从SDF文件中读取分子
+    conv.ReadFile(mol, input_sdf)
+
+    # 创建力场对象，使用MMFF94力场
+    forcefield = openbabel.OBForceField.FindForceField("MMFF94")
+
+    # 为分子设置力场
+    success = forcefield.Setup(mol)
+    if not success:
+        raise Exception("Error setting up force field")
+
+    # 进行能量最小化
+    forcefield.SteepestDescent(10000)  # 原来是5000步最速下降法
+    forcefield.GetCoordinates(mol)  # 将能量最小化后的坐标保存到分子对象
+
+    # 将能量最小化后的分子写入到SDF文件
+    conv.WriteFile(mol, output_sdf)
+    
+#%% 
+from tqdm import tqdm
+from concurrent.futures import ProcessPoolExecutor
+import multiprocessing
+
+def handle_file(filename):
+    if '.sdf' == filename[-4:]:
+        input_sdf_file = os.path.join(input_dirpath, filename)
+        output_sdf_file = os.path.join(output_dirpath, filename)
+        try:
+            sdf_min(input_sdf_file, output_sdf_file)
+        except Exception as e:
+            print(f"An error occurred while processing the file '{input_sdf_file}': {e}")
+            try:
+                os.remove(output_sdf_file)
+                print(output_sdf_file + ' was successfully removed')
+            except Exception:
+                if os.path.exists(output_sdf_file):
+                    print('please remove '+output_sdf_file)
+    else:
+        src_file = os.path.join(input_dirpath, filename)
+        dst_file = os.path.join(output_dirpath, filename)
+        shutil.copy(src_file, dst_file)
+
+def main():
+    file_list = os.listdir(input_dirpath)
+    # 获取系统的 CPU 核心数
+    num_cores = multiprocessing.cpu_count()
+
+    # 创建一个进程池
+    with ProcessPoolExecutor(max_workers=num_cores) as executor:
+        # 使用 tqdm 提供进度条功能
+        list(tqdm(executor.map(handle_file, file_list), total=len(file_list)))
+
+
+
+#%%
+import pandas as pd
+import os
+import hashlib
+class dir_check():
+    def __init__(self,dirpath):
+        self.dirpath = dirpath
+        self.mapping_file = os.path.join(self.dirpath, 'hash_ligand_mapping.csv')
+        self.mapping_data = pd.read_csv(self.mapping_file, header=None)
+        self.smiles_list = self.mapping_data.iloc[:, 1].tolist()
+        self.hash_list = self.mapping_data.iloc[:, 0].tolist()
+        self.filename_list = os.listdir(self.dirpath)
+        self.sdf_filename_list = [x for x in self.filename_list if x[-4:] == '.sdf']
+        
+    def mapping_file_check(self):
+        for i in range(len(self.smiles_list)):
+            if hashlib.sha1(self.smiles_list[i].encode()).hexdigest() != self.hash_list[i]:
+                print('error in mapping file')
+        print('mapping file check completed')
+        
+    def dir_file_check(self):
+        filename_hash_list = [x[:-4] for x in self.sdf_filename_list]
+        for filename_hash in filename_hash_list:
+            if filename_hash not in self.hash_list:
+                filename = filename_hash+'.sdf'
+                print(filename + ' not in mapping file')
+                os.remove(os.path.join(self.dirpath,filename))
+                print('remove ' + os.path.join(self.dirpath,filename))
+#%%      
+
+if __name__ == '__main__':
+    main()
+  
+    check = dir_check(output_dirpath)
+    check.mapping_file_check()
+    check.dir_file_check()   
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
+    
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